That all sounds really interesting! If you'd like any inspiration, @Worffan101 had a really good timeline a few years ago called Age of (near) Extinction detailing a lot of examples of OTL extinct species surviving. A lot of the posts are specifically about hominids like Neanderthals or Homo erectus surviving, which I feel would be a bit outside the scope of Atlas Altera, but there are also a lot of interesting pieces on other species surviving that you could possibly take inspiration from (with permission, of course).Yeah, that's similar to my line of thinking. I think Java, Sumatra, Iran etc. provide good examples of highly dense human populations living alongside megafauna and apex predators, even if the populations of those animals have become highly marginal and restricted to small pockets of areas. For the moas and elephant birds, I was thinking domestication due to the fact that the birds might not have a flight reflex to humans, and having the tweak that the Austronesians that discover the animals clue in quicker that herding the animals instead of striking them dead might be fruitful in the long run... For the saber tooths, I was hoping the Andes could help, and for the marsupials...well we have until colonialism to prove that they are viable, except Thylacoleo might need something...perhaps surviving in Cantabria (big Tasmania).
More specifically, I'd be interested in seeing if any other major megafauna in South America or Australia (the OTL continent, not Kerguelen) survived due to how unique these biospheres were, and in Australia specifically I'd be interested in how the inland sea's impacted different biomes and different lifeforms.
One more note is how these different animals might impact local cultures. Even IOTL there's some level of cultural memory of extinct animals like mammoths in the myths of various peoples in Siberia and North America, so having these animals survive could lead to some very interesting cultural developments.